Render background and freestyle in different image layers
As far as my understanding goes, Blender isn't capable of creating multilayered TIFFs.
However, you could use other software to acchieve that.
 1. Change the file format for the output
In Output Properties you would specify the file format &quot;TIFF&quot;.
Any file format that supports transparency (and can be converted by ImageMagick) should be fine.

 2. Assign Freestyle its own render pass 
Since Blender 2.83 there is an option to set Freestyle as a render pass in View Layer Properties.

In the compositor, Freestyle can then be processed separately.

In case you have multiple layers that you like to export in a single run, you could use File Output Nodes.
For the default cube, the rendered image would look something like this.

 3. Use other software to create a layered TIFF
Any software that is capable of creating multilayered TIFFs will work.
For ImageMagick this command should work. (As ImageMagick doesn't have a graphical user interface, this is executed from the command line.)
convert canvas:white -resize 1920x1080! blender_render.tif -compose over multilayered_result.tif


The resolution should match the resolution of your render.
Without the trailing exclamation mark, the background would keep its ratio (a square).